MolNFT v1 · #55536 · protein

Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor

2YNE · Glycylpeptide N-tetradecanoyltransferase: “Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor”. X-ray diffraction, 5 ligands (NHW, YNE, MG), 8 pockets (best druggability 0.81). MolNFT v1 #55536 on…

PDB: 2YNE
Type: protein
Length: 1,135 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycylpeptide N-tetradecanoyltransferase
EC: 2.3.1.97
UniProt: A5K1A2
Ligands: NHW, YNE, MG, CL, SO4
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	384	28% helix, 30% strand	A5K1A2
C	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	367	27% helix, 32% strand	A5K1A2

Ligands and binding sites

NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
YNE · 2-(3-piperidin-4-yloxy-1-benzothiophen-2-yl)-5-[(1,3,5-trimethylpyrazol-4-yl)methyl]-1,3,4-oxadiazole · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 4 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A, B
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.81	0.82	98	empty
2	824	0.80	0.82	73	NHW, YNE, MG
3	916	0.80	0.82	87	NHW, YNE, MG
4	902	0.79	0.81	83	NHW, YNE, MG
5	132	0.42	0.75	17	empty

Interfaces

2 interfaces between chains.

A–B · 436 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2YNE · Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A5K1A2
Elsewhere: RCSB PDB 2YNE · PDBe 2YNE · UniProt A5K1A2

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